Random coil conformations of polynucleotides: a study incorporating long-range correlations due to dynamics of the sugar residue

Sugar conformational effects on the photochemistry of thymidylyl(3'-5')thymidine

The synthesis and conformational analysis of 2'-O,5-dimethyluridylyl(3'-5')-2'-O,5-dimethyluridine (1a), the analogue of thymidylyl(3'-5')thymidine (TpT; 1b) in which a methoxy group replaces each 2'-alpha-hydrogen atom, are described. In comparison with TpT, such modification increases the population of the C3'-endo conformer of the sugar ring puckering at the 5'- and 3'-ends from 30 to 75% and from 37 to 66%, respectively. Photolyses of 1a and TpT at 254 nm are qualitatively comparable (the cis-syn cyclobutane pyrimidine dimer and the (6-4) photoproduct are formed), although it is significantly faster in the case of 1a. These results are explained by the increased propensity of the modified dinucleotide to adopt a base-stacked conformation geometry reminiscent of that for TpT.

Backbone conformation in nucleic acids: an analysis of local helicity through heminucleotide scheme and a proposal for a unified conformational plot

A relationship has been established to express the local helicity of a polynucleotide backbone directly in terms of the virtual bonds spanning the conformationally equivalent heminucleotide repeats, with a view to provide a better understanding of the cumulative effects of all the chemical bond rotational variations on local helicity. Using this, an analysis made with a few oligodeoxynucleotide crystal structures clearly brings forth that it is the concerted movements manifested in the near neighbour correlations between the pair of chemical bonds C4'-C5' and P-O5' and C4'-C3' and P-O3' of the 5' and 3' heminucleotides respectively that are primarily responsible for the observed non-uniform helical twists both in A and B type helical backbones. That these need not be restricted to oligodeoxynucleotides but may be a feature of oligoribonucleotides backbone also is shown from an analysis of helical segments of yeast tRNA(Phe). A proposal of a unified or a grand two dimensional conformational plot which would help visualise succinctly the overall effect of the variations in all the repeating six chemical bonds of a polynucleotide backbone is made. Apart from considerable simplification, the plot affords identification on it regions characteristic of helical, and loop and bend conformations of nucleic acid backbone chain.